[English] 日本語
Yorodumi
- PDB-2lfv: Solution Structure of the SPOR domain from E. coli DamX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lfv
TitleSolution Structure of the SPOR domain from E. coli DamX
ComponentsProtein damX
KeywordsCELL CYCLE / cell division / peptidoglycan binding domain / murein binding domain / bacterial cell division protein / RNP fold / RNP domain
Function / homology
Function and homology information


cytokinetic process / peptidoglycan binding / cell septum / cell division site / plasma membrane => GO:0005886
Similarity search - Function
Cell division protein DamX / Sporulation related repeat / Sporulation-like domain / Sporulation-like domain superfamily / SPOR domain / SPOR domain profile. / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein DamX
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsWilliams, K.B. / Arends, S.J.R. / Popham, D.L. / Fowler, C.A. / Weiss, D.S.
CitationJournal: Biochemistry / Year: 2013
Title: Nuclear Magnetic Resonance Solution Structure of the Peptidoglycan-Binding SPOR Domain from Escherichia coli DamX: Insights into Septal Localization.
Authors: Williams, K.B. / Yahashiri, A. / Arends, S.J. / Popham, D.L. / Fowler, C.A. / Weiss, D.S.
History
DepositionJul 15, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED. PROLINE 407 REMOVED FROM HELIX.
Remark 700SHEET DETERMINATION METHOD: AUTHOR BASED UPON 1. THE REGION OF RAMACHANDRAN SPACE EACH INDIVIDUAL ...SHEET DETERMINATION METHOD: AUTHOR BASED UPON 1. THE REGION OF RAMACHANDRAN SPACE EACH INDIVIDUAL RESIDUE FALLS INTO (PROCHECK AND TALOS) 2. CHEMICAL SHIFT INDEX VALUES (RE-CONFIRMED WHILE LOOKING OVER THE BMRB RESPONSE) 3. VISUAL INSPECTION AND 4. COMPARISON/CONSISTENCY WITH OTHER SPOR DOMAINS AS WELL AS SEVERAL OTHER RNP FOLD PROTEINS.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein damX


Theoretical massNumber of molelcules
Total (without water)11,8761
Polymers11,8761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 250structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Protein damX


Mass: 11876.159 Da / Num. of mol.: 1 / Fragment: sequence database residures 338-428
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 MG1655 / Gene: b3388, damX, yhfB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11557

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HMQC
1333D HNCA
1433D HN(CO)CA
1533D HN(CA)CB
1633D CBCA(CO)NH
1733D HNCO
1833D HN(CA)CO
1913D 1H-15N TOCSY
11013D 1H-15N NOESY
11122D DQF-COSY
11222D 1H-1H NOESY
11322D 1H-1H TOCSY
11433D C(CO)NH
11533D H(CCO)NH
1162(HB)CB(CGCD)HE
1172(HB)CB(CGCDCE)HE
11823D 1H-13C NOESY
11933D 1H-13C NOESY
12023D (H)CCH-TOCSY
12112D 1H-15N IPAP HSQC
12242D 1H-15N IPAP HSQC
12312D 15N T1
12412D 15N T2
12512D {1H}-15N NOE
NMR detailsText: The SPOR domain consists of residues 344-428. Structure analysis and statistics in the accompanying publication consider only this portion of the construct. Residues 323-338 are poorly ...Text: The SPOR domain consists of residues 344-428. Structure analysis and statistics in the accompanying publication consider only this portion of the construct. Residues 323-338 are poorly constrained and represent a His-tag plus linker; this region accounts for roughly half of the close contacts and Ramachandran outliers noted in this file.

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-99% 15N] DamX SPOR domain polypeptide, 50 mM potassium phosphate, 50 mM potassium chloride, 90 % H2O, 10 % [U-99% 2H] D2O90% H2O/10% D2O
20.7 mM [U-99% 13C; U-99% 15N] DamX SPOR domain polypeptide, 50 mM potassium phosphate, 50 mM potassium chloride, 100 % [U-99% 2H] D2O100% D2O
30.7 mM [U-99% 13C; U-99% 15N] DamX SPOR domain polypeptide, 50 mM potassium phosphate, 50 mM potassium chloride, 90 % H2O, 10 % [U-99% 2H] D2O90% H2O/10% D2O
40.7 mM [U-99% 15N] DamX SPOR domain polypeptide, 50 mM potassium phosphate, 50 mM potassium chloride, 5 % PEG(C12E5):n-hexanol, 90 % H2O, 10 % [U-99% 2H] D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMDamX SPOR domain polypeptide-1[U-99% 15N]1
90 %H2O-21
10 %D2O-3[U-99% 2H]1
50 mMpotassium phosphate-41
50 mMpotassium chloride-51
0.7 mMDamX SPOR domain polypeptide-6[U-99% 13C; U-99% 15N]2
100 %D2O-7[U-99% 2H]2
50 mMpotassium phosphate-82
50 mMpotassium chloride-92
0.7 mMDamX SPOR domain polypeptide-10[U-99% 13C; U-99% 15N]3
90 %H2O-113
10 %D2O-12[U-99% 2H]3
50 mMpotassium phosphate-133
50 mMpotassium chloride-143
0.7 mMDamX SPOR domain polypeptide-15[U-99% 15N]4
90 %H2O-164
10 %D2O-17[U-99% 2H]4
50 mMpotassium phosphate-184
50 mMpotassium chloride-194
5 %PEG(C12E5):n-hexanol-204
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
VnmrJ2.1BVariancollection
CCPN_Analysis1.0.15CCPNpeak picking
CCPN_Analysis1.0.15CCPNchemical shift assignment
CCPN_Analysis1.0.15CCPNdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
curvefitPalmerdata analysis
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorerefinement
ProcheckNMR3.5.4Laskowski and MacArthurstructure analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2810 / NOE intraresidue total count: 894 / NOE long range total count: 673 / NOE medium range total count: 353 / NOE sequential total count: 533 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 81 / Protein psi angle constraints total count: 81
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 25 / Torsion angle constraint violation method: XPLOR-NIH

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more